These are chat archives for dereneaton/ipyrad

31st
Mar 2017
Isaac Overcast
@isaacovercast
Mar 31 2017 12:58 UTC
@dereneaton @jenarch Another thing that could be causing this behavior is disk limits getting hit. If you hit your quota then all kinds of funny stuff could happen like files not getting created and processes sitting around waiting forever. Assemblies can get really big. Do you have a disk quota (I know we have quotas on my cluster).
Isaac Overcast
@isaacovercast
Mar 31 2017 13:14 UTC
@Cycadales_twitter This looks highly irregular:
## The number of loci recovered for each Sample.
## ipyrad API location: [assembly].stats_dfs.s7_samples

                                   sample_coverage
Cmac-15-10-1-R_S18001_PairedTrim            188146
Cmac-15-10-10-R_S17001_PairedTrim           188146
Cmac-15-10-2-R_S19001_PairedTrim            188146
Cmac-15-10-3-R_S20001_PairedTrim            188146
Cmac-15-10-4-R_S21001_PairedTrim            188146
Cmac-15-10-5-R_S22001_PairedTrim            188146
Something got goofed up somewhere. The stats look good through step 5. It's hard so say whether the divide by zero error is a cause or an effect of the real problem. Can you re-run step 6 with the -d flag and email me the ipyrad_log.txt?
James Clugston
@Cycadales_twitter
Mar 31 2017 13:35 UTC
@isaacovercast Yea I know that one is not quite right! But it was all I could download last night. looks like all the other steps from 1-5 are fine or at leas to me do not look unusual. The other steps are fine but something seems to be happening during sep six.
James Clugston
@Cycadales_twitter
Mar 31 2017 13:42 UTC
I will run step six over the weekend and see it spits out
Jenny Archibald
@jenarch
Mar 31 2017 21:30 UTC
@isaacovercast @dereneaton Thanks both for your advice! I've asked our cluster help about disk limits and am trying again with fewer cores per node as well as a run with more stringent filtering. Hopefully one of them works!
natagalle
@natagalle
Mar 31 2017 23:50 UTC
Hello @isaacovercast @dereneaton I noticed in my .loci file that I have many invariant loci across a sample of 100 individuals. Is this normal? Is there a way to filter these loci out? Thanks!!